Introduction to Chemistry Concepts

Chemical Biology and Biomolecules

• Chemical biology is an interdisciplinary field combining chemistry and biology
• It studies chemical processes within living systems
• The primary focus is understanding biological systems at the molecular level
• Applications are found in drug discovery, biotechnology, and medicine

Biochemistry

• Biochemistry is the study of structure, composition and chemical reactions in living things
• Living organisms, or biotic factors, depend on chemistry for survival, demonstrating the close relationship between biology and chemistry

Fundamental Biomolecules

• Four major classes of biomolecules are proteins, nucleic acids, carbohydrates, and lipids
• Each class fulfills unique biological functions
• They are all essential for life processes

Organic Chemistry

• Organic chemistry is the study of carbon and hydrogen compounds (hydrocarbons) and their derivatives

Atomic Structure

• Atoms are composed of subatomic particles: protons, neutrons, and electrons
• Protons have a positive charge and are part of the nucleus.
• Neutrons have no charge and are part of the nucleus.
• Electrons have a negative charge and orbit the nucleus.
• Atomic mass is the sum of protons and neutrons
• Electrons do not contribute mass
• Atomic number is the number of protons
• The number of protons in an atom determines the number of electrons in the atom

Molecules and Compounds

• A molecule is formed when two or more atoms chemically combine
• A compound forms when two or more atoms of different elements chemically combine indefined proportions
• Molecular formulas show the elements present in a molecule and their respective quantities

Isotopes

• Isotopes are atoms of the same element with the same number of protons but a different number of neutrons
• Isotopes have the same atomic number but different atomic weights
• Examples of oxygen isotopes are O16, O17, and O18
• Unstable isotopes are radioactive and emit energy, used in medicine and research

Radioactive Tracers

• PET scans utilize radioactive isotopes to detect locations of high chemical activity in the body
• Bright yellow spots on a PET scan indicated heightened metabolic activity, a sign of possible cancerous tissue.
• The radioactive tracer is often a glucose molecule

Water: The Solvent for Biochemical Reactions

• Properties of Water:
• Hydrogen Bonds: Positive charges on one water molecule and negative charges on an adjacent water molecule attract each other, forming hydrogen bonds. These bonds cause water to exhibit characteristic traits.
• Cohesion: Water molecules stick together due to hydrogen bonds. Cohesion helps water flow from roots to leaves in plants.
• Adhesion: Water sticks to other polar surfaces. Adhesion is vital for capillary action.
• Surface Tension: Hydrogen bonds create strong surface tension, allowing some insects to walk on water.
• Density: Water is denser than ice, allowing ice to float and act as insulation in water bodies.
• Solubility (Universal Solvent): Water is a universal solvent due to its polarity. The polar nature of water enables it to dissolve many substances. Substances dissolved in water form solutions. The substance being dissolved is called a solute, while a substance that dissolves another is called a solvent.

Membrane and Membrane Transport

• Cell membranes are fluid mosaics of lipids and proteins
• Phospholipids are the most abundant lipids in cell membranes
• Phospholipids are amphipathic; they have both a hydrophilic ("water-loving") region and a hydrophobic ("water-dreading") region
• The cell membrane's structure is described by the fluid mosaic model
• Membrane proteins:
  • Some membrane proteins are integral and permanently embedded in the membrane. Other proteins exist as peripheral proteins, which are found temporarily attached to the membrane's surface or to other integral proteins.
  • Integral proteins can span the membrane (transmembrane proteins).
  • They also may be lipid-anchored or monotopic
  • Peripheral proteins are often involved in intercellular joining, attachment to cytoskeleton and ECM, and are sometimes involved in signal transduction and transport
• Membrane proteins play significant roles in diverse cellular functions: signaling, transport (active and passive), enzymatic activity, cell-cell recognition and intercellular joining.
• Carbohydrates found on the exterior of cell membranes, either attached to proteins (glycoproteins) or lipids (glycolipids).
  • Carbohydrates provide sites for cell recognition, enabling cells to identify and interact with each other.

Transport Mechanisms

• Passive Transport: Does not require energy, relies on the concentration gradient. Types include: diffusion, osmosis, and facilitated diffusion (assisted by a carrier protein)
• Active Transport: Requires energy (ATP) to move molecules against the concentration gradient. Types include: primary active transport (e.g., sodium-potassium pump) and secondary active transport.
• Bulk Transport: Requires energy. Types include endocytosis (materials entering the cell), exocytosis (materials exiting the cell), pinocytosis (absorbing dissolved substances), and phagocytosis (absorbing whole particles or cells).